MusicBee 3.3.7310, library is on a NAS, accessed through NFS.
Here's what I did:
1. I had an album with the following folder structure:
Album/CD1/
Album/CD2/
2. I used "Send to" > "Move files to organised folder" to move all the tracks into "Album/" along with any remaining non-media files.
3. I notice that the CD1 folder disappeared, however the CD2 folder is still present (and empty). If I remove it, it reappears as soon as MusicBee is focused.
I assume something, somewhere is still pointing to the folder and that's why it keeps reappearing. This happens with all albums I restructured.